CUQIpy 0.5.0.post0.dev27__py3-none-any.whl → 0.5.0.post0.dev34__py3-none-any.whl

{CUQIpy-0.5.0.post0.dev27.dist-info → CUQIpy-0.5.0.post0.dev34.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CUQIpy
-Version: 0.5.0.post0.dev27
+Version: 0.5.0.post0.dev34
 Summary: Computational Uncertainty Quantification for Inverse problems in Python
 Maintainer-email: "Nicolai A. B. Riis" <nabr@dtu.dk>, "Jakob S. Jørgensen" <jakj@dtu.dk>, "Amal M. Alghamdi" <amaal@dtu.dk>
 License: Apache License
@@ -213,70 +213,94 @@ Requires-Dist: arviz
 
 [![pytest](https://github.com/CUQI-DTU/CUQIpy/actions/workflows/tests.yml/badge.svg)](https://github.com/CUQI-DTU/CUQIpy/actions/workflows/tests.yml)
 [![docs](https://github.com/CUQI-DTU/CUQIpy/actions/workflows/docs.yml/badge.svg)](https://cuqi-dtu.github.io/CUQIpy/)
+[![PyPI](https://github.com/CUQI-DTU/CUQIpy/actions/workflows/publish_pypi.yml/badge.svg)](https://pypi.org/project/CUQIpy/#history)
 
-Computational Uncertainty Quantification for Inverse Problems in python (CUQIpy) is a python package for modeling and solving inverse problems in a Bayesian inference framework. CUQIpy provides a simple high-level interface to perform UQ analysis of inverse problems, while still allowing full control of the models and methods. The package comes equipped with a number of predefined distributions, samplers, models and test problems and is built to be easily further extended when needed.
+**CUQIpy** stands for Computational Uncertainty Quantification for Inverse Problems in python. It's a robust Python package designed for modeling and solving inverse problems using Bayesian inference. Here's what it brings to the table:
 
-You can find the full CUQIpy documentation [here](https://cuqi-dtu.github.io/CUQIpy/). 
+- A straightforward high-level interface for UQ analysis.
+- Complete control over the models and methods.
+- An array of predefined distributions, samplers, models, and test problems.
+- Easy extendability for your unique needs.
 
-This software package is part of the [CUQI project](https://www.compute.dtu.dk/english/cuqi) funded by [the Villum Foundation.](https://veluxfoundations.dk/en/forskning/teknisk-og-naturvidenskabelig-forskning)
+CUQIpy is part of the [CUQI project](https://www.compute.dtu.dk/english/cuqi) supported by the [Villum Foundation.](https://veluxfoundations.dk/en/forskning/teknisk-og-naturvidenskabelig-forskning)
 
-## Quickstart
+## 📚 Resources
+
+- **Documentation:** [CUQIpy website](https://cuqi-dtu.github.io/CUQIpy/)
+
+- **Papers:** CUQIpy on ArXiv - [Part I](https://arxiv.org/abs/2305.16949) & [Part II](https://arxiv.org/abs/2305.16951)
+
+- **Training:** [Demo & training notebooks](https://github.com/CUQI-DTU/CUQIpy-demos)
+
+
+## 🚀 Quickstart
 Install CUQIpy using pip:
 ```{r, engine='bash', count_lines}
 pip install cuqipy
 ```
 For more detailed instructions, see the [Getting Started](https://cuqi-dtu.github.io/CUQIpy/user/getting_started.html) guide.
 
-## Quick Example - UQ in 5 steps
-Image deconvolution with uncertainty quantification
+## 🧪 Quick Example - UQ in a few lines of code
+Experience the simplicity and power of CUQIpy with this Image deconvolution example. Getting started with UQ takes just a few lines of code:
 ```python
 # Imports
-import numpy as np
 import matplotlib.pyplot as plt
 from cuqi.testproblem import Deconvolution2D
-from cuqi.data import grains
-from cuqi.distribution import LMRF, Gaussian
+from cuqi.distribution import Gaussian, LMRF, Gamma
 from cuqi.problem import BayesianProblem
 
-# Step 1: Model and data, y = Ax
-A, y_data, info = Deconvolution2D.get_components(dim=128, phantom=grains())
-
-# Step 2: Prior, x ~ LMRF(0,0.01)
-x = LMRF(location=0,
-         scale=0.01,
-         bc_type='neumann',
-         geometry = A.domain_geometry)
+# Step 1: Set up forward model and data, y = Ax
+A, y_data, info = Deconvolution2D.get_components(dim=256, phantom="cookie")
 
-# Step 3: Likelihood, y ~ N(Ax, 0.0036^2)
-y = Gaussian(mean=A@x, cov=0.0036**2)
+# Step 2: Define distributions for parameters
+d = Gamma(1, 1e-4)
+s = Gamma(1, 1e-4)
+x = LMRF(0, lambda d: 1/d, geometry=A.domain_geometry)
+y = Gaussian(A@x, lambda s: 1/s)
 
-# Step 4: Set up Bayesian problem and sample posterior
-BP = BayesianProblem(y, x).set_data(y=y_data)
+# Step 3: Combine into Bayesian Problem and sample posterior
+BP = BayesianProblem(y, x, d, s)
+BP.set_data(y=y_data)
 samples = BP.sample_posterior(200)
 
-# Step 5: Analysis
-info.exactSolution.plot(); plt.title("Exact solution")
-y_data.plot(); plt.title("Data")
-samples.plot_mean(); plt.title("Posterior mean")
-samples.plot_std(); plt.title("Posterior standard deviation")
+# Step 4: Analyze results
+info.exactSolution.plot(); plt.title("Sharp image (exact solution)")
+y_data.plot(); plt.title("Blurred and noisy image (data)")
+samples["x"].plot_mean(); plt.title("Estimated image (posterior mean)")
+samples["x"].plot_std(); plt.title("Uncertainty (posterior standard deviation)")
+samples["s"].plot_trace(); plt.suptitle("Noise level (posterior trace)")
+samples["d"].plot_trace(); plt.suptitle("Regularization parameter (posterior trace)")
 ```
 
 <p float="left">
-<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_exact_sol.png" alt="Exact solution" width="330">
-<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_data.png" alt="Data" width="330">
-<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_post_mean.png" alt="Posterior mean" width="330">
-<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_post_std.png" alt="Posterior standard deviation" width="330">
+<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_exact_sol.png" alt="Sharp image (exact solution)" width="330">
+<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_data.png" alt="Blurred and noisy image (data)" width="330">
+<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_post_mean.png" alt="Estimated image (posterior mean)" width="330">
+<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_post_std.png" alt="Uncertainty (posterior standard deviation)" width="330">
+<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_noise_level.png" alt="Noise level (posterior trace)" width="660">
+<img src="https://cuqi-dtu.github.io/CUQIpy/_images/deconv2D_regularization_parameter.png" alt="Regularization parameter (posterior trace)" width="660">
 </p>
 
-## Plugins
-CUQIpy can be extended with additional functionality by installing optional plugins. These can be found at
-[CUQI-DTU](https://github.com/CUQI-DTU?q=CUQIpy-).
+## 🔌 Plugins
+CUQIpy can be extended with additional functionality by installing optional plugins. We currently offer the following plugins:
 
-## Contributing
+- [CUQIpy-CIL](https://github.com/CUQI-DTU/CUQIpy-CIL) A plugin for the Core Imaging Library [(CIL)](https://ccpi.ac.uk/cil/) providing access to forward models for X-ray computed tomography.
+
+- [CUQIpy-FEniCS](https://github.com/CUQI-DTU/CUQIpy-FEniCS): A plugin providing access to the finite element modelling tool [FEniCS](https://fenicsproject.org), which is used for solving PDE-based inverse problems.
+
+- [CUQIpy-PyTorch](https://github.com/CUQI-DTU/CUQIpy-PyTorch): A plugin providing access to the automatic differentiation framework of [PyTorch](https://pytorch.org) within CUQIpy. It allows gradient-based sampling methods without manually providing derivative information of distributions and forward models.
+
+## 🤝 Contributing
 We welcome contributions to CUQIpy. Please see our [contributing guidelines](https://cuqi-dtu.github.io/CUQIpy/dev/index.html) for more information.
 
-## Contributors
+## 💻 Developers
+
+[Nicolai André Brogaard Riis](https://github.com/nabriis)
+[Amal Mohammed A Alghamdi](https://github.com/amal-ghamdi)
+[Chao Zhang](https://github.com/chaozg)
+[Jakob Sauer Jørgensen](https://github.com/jakobsj)
+
+## 🌟 Contributors
 
-See the list of
-[contributors](https://github.com/CUQI-DTU/CUQIpy/graphs/contributors)
-who participated in this project.
+A big shoutout to our passionate team! Discover the talented individuals behind CUQIpy
+[here](https://github.com/CUQI-DTU/CUQIpy/graphs/contributors).

{CUQIpy-0.5.0.post0.dev27.dist-info → CUQIpy-0.5.0.post0.dev34.dist-info}/RECORD

@@ -1,12 +1,12 @@
 cuqi/__init__.py,sha256=K0ss2HNqoLUX7wGpSZdaPKxIaKdRS452fcJm4D0pcEs,433
 cuqi/_messages.py,sha256=fzEBrZT2kbmfecBBPm7spVu7yHdxGARQB4QzXhJbCJ0,415
-cuqi/_version.py,sha256=KBCwnCuvxt9C0BYthYMf_0rB_yxJdt6n9h2hnWAPLpE,509
+cuqi/_version.py,sha256=YG7wYnRbkAbc5L66X7naOLB81WxNl5GSQQD7Rjku_I8,509
 cuqi/config.py,sha256=wcYvz19wkeKW2EKCGIKJiTpWt5kdaxyt4imyRkvtTRA,526
 cuqi/diagnostics.py,sha256=5OrbJeqpynqRXOe5MtOKKhe7EAVdOEpHIqHnlMW9G_c,3029
 cuqi/array/__init__.py,sha256=-EeiaiWGNsE3twRS4dD814BIlfxEsNkTCZUc5gjOXb0,30
 cuqi/array/_array.py,sha256=Xm2n1MFnLhR3KUjoCzMc-tnZ5HBX1mQ8MyxhZnIvSCA,4400
 cuqi/data/__init__.py,sha256=1aGgPmtG_Kqbb880vLnPksGvyYQB_6o2mz_q-4KGYaU,173
-cuqi/data/_data.py,sha256=iF1DRD2LbMvYTuQY_XRvE_SUOegubXiaH8JLUjtgYmk,10689
+cuqi/data/_data.py,sha256=PgdYJ6MHgNY37Ak8wUYwvxcAwOYSNjnf1-BXMdbnuv4,10716
 cuqi/data/astronaut.npz,sha256=vVTb6eJLMZhrEZuOYzQWN3V2EhhVH6sHzrrf_7mstcw,786696
 cuqi/data/camera.npz,sha256=EznyKfAomn4orm-L9gqM3QDFNuGB5XZwpZZMwDgiMKk,262408
 cuqi/data/cat.npz,sha256=9H9iJqkvlCCVZZ2IWMfwwfVHbShpQTkZo_WGr7rrp3k,406164
@@ -63,8 +63,8 @@ cuqi/testproblem/_testproblem.py,sha256=x769LwwRdJdzIiZkcQUGb_5-vynNTNALXWKato7s
 cuqi/utilities/__init__.py,sha256=EfxHLdsyDNugbmbzs43nV_AeKcycM9sVBjG9WZydagA,351
 cuqi/utilities/_get_python_variable_name.py,sha256=QwlBVj2koJRA8s8pWd554p7-ElcI7HUwY32HknaR92E,1827
 cuqi/utilities/_utilities.py,sha256=rjycaxDWExdskIfYXV1z5ZlB0JTlqv3tCmKf08i6U5c,7973
-CUQIpy-0.5.0.post0.dev27.dist-info/LICENSE,sha256=kJWRPrtRoQoZGXyyvu50Uc91X6_0XRaVfT0YZssicys,10799
-CUQIpy-0.5.0.post0.dev27.dist-info/METADATA,sha256=VmLB0uLWuBTWHxKhGvup-YVyqJuufN0jy3PfqU6nRdw,16421
-CUQIpy-0.5.0.post0.dev27.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-CUQIpy-0.5.0.post0.dev27.dist-info/top_level.txt,sha256=AgmgMc6TKfPPqbjV0kvAoCBN334i_Lwwojc7HE3ZwD0,5
-CUQIpy-0.5.0.post0.dev27.dist-info/RECORD,,
+CUQIpy-0.5.0.post0.dev34.dist-info/LICENSE,sha256=kJWRPrtRoQoZGXyyvu50Uc91X6_0XRaVfT0YZssicys,10799
+CUQIpy-0.5.0.post0.dev34.dist-info/METADATA,sha256=KvQwyxbFj4m1wYkmXxgwjTW2DH6WHKigrqCoKhrTlPM,18348
+CUQIpy-0.5.0.post0.dev34.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+CUQIpy-0.5.0.post0.dev34.dist-info/top_level.txt,sha256=AgmgMc6TKfPPqbjV0kvAoCBN334i_Lwwojc7HE3ZwD0,5
+CUQIpy-0.5.0.post0.dev34.dist-info/RECORD,,

cuqi/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-10-04T08:52:20+0200",
+ "date": "2023-10-06T17:16:50+0200",
  "dirty": false,
  "error": null,
- "full-revisionid": "716b4d41cefac22fd6f6604b31714a21b72bad81",
- "version": "0.5.0.post0.dev27"
+ "full-revisionid": "900bab604f6c0683ac7ffd1f2a912296b85e5467",
+ "version": "0.5.0.post0.dev34"
 }
 '''  # END VERSION_JSON
 

cuqi/data/_data.py

@@ -350,11 +350,13 @@ def cookie(size=128, grayscale=True):
     # Convert to grayscale
     if grayscale:
         cookie = rgb2gray(cookie)
-        cookie[cookie < 0.05] = 0 # Make background completely black
-
+        
     # Resize
     cookie = imresize(cookie, size)
 
+    if grayscale:
+        cookie[cookie < 0.05] = 0 # Make background completely black
+
     return cookie
 
 def rgb2gray(img):